EcoCyc vs Sleep

Those of you who know me are probably well aware that I'm not a morning person, and that I'm not known for my early morning starts. I did get up once at 2.30 am in the morning in order to get to Masada in time to climb it and see the sunrise, and I was awake at 5 am in order to watch the sunrise at Angkor Wat. But this morning I've had 2 hours sleep, and woken up at 1.30 am, and I have a 10.5 hour skype call ahead of me. The reason for my sleep deprivation is that our annual EcoCyc Steering Committee Meeting is occurring today in San Francisco. Unfortunately, I wasn't able to attend in person, as I needed to be in Sydney to mark the exams for my CBMS336 Molecular Biology and Genomics unit. So I have the joy of attending via skype.

I have been a collaborator on the EcoCyc project since 1996 when I met Peter Karp at a conference at Lake Arrowhead and we discussed adding transport reactions to the EcoCyc database. EcoCyc is an online database for the bacterium E. coli, where all of the genes, proteins, metabolic pathways, transporters and regulatory pathways are described. The project combines computationally modeling everything we know about E. coli biology with reading all of the scientific literature published on E. coli and summarizing it in EcoCyc (curation). The role of my group  on the project is twofold- 1. we make sure that all membrane proteins and functions are represented in EcoCyc; 2. we participate in computationally testing the metabolic model of E. coli represented in EcoCyc to test its accuracy.

Anyway , as part of our funding from the National Institutes of Health (NIH) we have a Steering Committe which meets annually to advise us, which I am currently attending via skype. Hopefully I stay awake at least long enough to give my presentation to the committee, which is probably around 5-6 am my time.

Overview of the metabolic map of E. coli from EcoCyc